Showing papers on "Transcription (biology) published in 1978"
TL;DR: The author revealed that RNA polymerase mutations located at the Site of Termination Site are linked to RHO mutations, and that pN acts at Many Sites and recognition Specificity of pN is recognized.
Abstract: PERSPECTIVES AND SUMMARY 967 WHAT IS TRANSCRIPTION TERMINATION? 96S RHO-INDEPENDENT TERMINATION 969 RHO-DEPENDENT TERMINATION 972 THE SEQUENCES OF SOME TRANSCRIPTION TERMINATION SIGNALS.. 974 THE MECHANISM OF ACTION OF RHO ... 979 TRANSCRIPTION TERMINATION IN VIVO: A MODEL 9S2 Polarity: Transcription Termination with Operons ... ... .... 982 The Model 982 MUTATIONS AFFECTING TRANSCRIPTION TERMINATION 986 Mutations Located at the Site of Termination 986 Mutations Not Linked to the Affected Termination Site 986 RNA polymerase mutations 986 RHO mutations 986 ANTITERMINATION , ........ ..... ........ , 989 pN Acts at Many Sites 989 Recognition Specificity of pN 990 Stoichiometry of pN Requirement ..... ......... ..... ... .... ......... 991 Involvement of Host Factors 992 Bypass of pN Requirement , .. , ... , ,." .. , .. ,........ 992 Models of Antitermination .. , , .. ,.,., , ,., .. ,...... 993
550 citations
TL;DR: These data on conservation of the Ad2 sequences suggest that each transcriptional event from the 16-99 transcription unit gives rise to one of a possible 13-14 mRNA molecules with destruction of the remainder of the transcribed RNA.
385 citations
370 citations
TL;DR: Strong homologies at cap sites and splice points suggest that for the noted cases, the virus and cell share closely related mechanisms for mRNA 5' end synthesis and splicing.
335 citations
TL;DR: The mechanism of rifampicin inhibition of Escherichia coli RNA polymerase was studied with a newly developed steady state assay for RNA chain initiation and by analysis of the products formed with several 5'-terminal nucleotides.
302 citations
TL;DR: It is shown that wild-type yeast contains such an enzymatic activity, and that this activity specifically removes the intervening sequences to produce mature-sized RNAs.
267 citations
TL;DR: It is proposed that the alpha-amanitin sensitivity of viral RNA transcription in vivo is explained by initiation by primer RNAs synthesized by the host cell, specifically by RNA polymerase II, thereby explaining thealpha-amanitized virus-specific proteins sensitivity in vivo.
Abstract: Because influenza viral RNA transcription in vitro is greatly enhanced by the addition of a primer dinucleotide, ApG or GpG, we have proposed that viral RNA transcription in vivo requires initiation by primer RNAs synthesized by the host cell, specifically by RNA polymerase II, thereby explaining the α-amanitin sensitivity of viral RNA transcription in vivo. Here, we identify such primer RNAs, initially in reticulocyte extracts, where they are shown to be globin mRNAs. Purified globin mRNAs very effectively stimulated viral RNA transcription in vitro, and the resulting transcripts directed the synthesis of all the nonglycosylated virus-specific proteins in micrococcal nuclease-treated L cell extracts. The viral RNA transcripts synthesized in vitro primed by ApG also directed the synthesis of the nonglycosylated virus-specific proteins, but the globin mRNA-primed transcripts were translated about 3 times more efficiently. The translation of the globin mRNA-primed, but not the ApG-primed, viral RNA transcripts was inhibited by 7-methylguanosine 5′-phosphate in the presence of S-adenosylhomocysteine, suggesting that the globin mRNA-primed transcripts contained a 5′-terminal methylated cap structure. We propose that this cap was transferred from the globin mRNA primer to the newly synthesized viral RNA transcripts, because no detectable de novo synthesis of a methylated cap occurred during globin mRNA-primed viral RNA transcription. Preliminary experiments indicate that other purified eukaryotic mRNAs also stimulate influenza viral RNA transcription in vitro.
265 citations
TL;DR: Values indicate very rapid transcription rates (greater than 20 transcripts per min) and exceptionally fast processing rates (approximately 0.5 min for the primary transcripts and approximately 5 min for overall nuclear processing) for the Ig mRNAs, which account for the high abundance of Ig m RNAs in the myeloma cell.
252 citations
TL;DR: Inhibition of transcription by intermediate concentrations of alpha-amanitin demonstrates that RNA polymerase III transcribes at least 90% of all RNA synthesized.
245 citations
TL;DR: Comparison of the in vitro expression of portions of the ovalbumin gene in nuclei isolated from chronically stimulated oviducts indicates that both structural and intervening sequences are preferentially transcribed in vitro at rates approximately 500 times greater than expected for random transcription of the haploid chick genome.
213 citations
TL;DR: This chapter illustrates that crude homogenates and crude nuclei have minimal RNA synthetic activity but activity becomes evident on further purification, and in each system careful evaluation of conditions for optimal activity is required and they may well vary extensively.
Abstract: Publisher Summary This chapter describes a system that fulfills many of the requirements for the study of gene control in vitro. The system makes possible the study of the primary transcription event separate from later maturation and transport events in RNA synthesis. While the results in the chapter are described for myeloma cells, lines derived from the MPC-11 tumor, the preliminary results with chick embryos, and those of others with HeLa cells and other myeloma cells suggest that these methods may be generally applicable. There are many examples of systems of isolated nuclei where the RNA product is small. Moreover, the isolated nuclei synthesize a very small product, but the nuclear subfraction they isolate (nucleoli) synthesizes very large RNA. This chapter illustrates that crude homogenates and crude nuclei have minimal RNA synthetic activity but activity becomes evident on further purification. Thus, in each system careful evaluation of conditions for optimal activity is required and they may well vary extensively.
TL;DR: It is concluded that the mutations define a new kind of recognition site (which the authors designate nut , for N utilization ) that controls an early step in the N-mediated antitermination mode of transcription.
TL;DR: The results of attempts to determine the sequence relationship between vRNAs and the two classes of complementary RNA synthesized in influenza infected cells are described which support the conclusion that influenza messenger RNAs are incomplete transcripts.
Abstract: The results of analyses of the 5'-terminal sequences of Fowl Plague virus RNAs are presented. The first 13 residues of each of the eight RNA molecules which constitute the genome are in the identical sequence 5'AGUAGAAAUUAGG- and this conservation of sequence is shown to extend to other influenza viruses. The 5'-terminal sequences of virion RNA transcripts produced in vitro are also reported and again the first 12 nucleotides of these are identical for all influenza type A transcripts examined in the sequence 5'AGCAAAAGCAGG-. In addition the results of attempts to determine the sequence relationship between vRNAs and the two classes of complementary RNA synthesized in influenza infected cells are described which support the conclusion that influenza messenger RNAs are incomplete transcripts.
TL;DR: Sixteen bacterial clones containing sequences complementary to yeast PhetRNA were isolated from a collection of hybrid plasmids containing BamHI restriction endonuclease-generated yeast DNA fragments inserted in the plasmid vector pBR315, reporting the sequence of the Phe-tRNA structural genes and adjacent regions of three of these clones.
Abstract: Sixteen bacterial clones containing sequences complementary to yeast PhetRNA were isolated from a collection of hybrid plasmids containing BamHI restriction endonuclease-generated yeast DNA fragments inserted in the plasmid vector pBR315. Ten of these clones contained hybrid plasmids with distinct BamHI fragments. The sequence of the Phe-tRNA structural genes and adjacent regions of three of these clones is reported here. In the region flanking the tRNA gene, the sequence of two of the cloned DNAs is similar; the sequence of the third varies considerably. All three of the tRNA genes are bordered by A,T-rich regions. In particular, near the region coding for the 3' end of the tRNA there is a long sequence of As in the coding strand. This is reminiscent of the region of termination of transcription of the yeast 5S rRNA gene. The sequences coding for the Phe-tRNA contain an additional segment of 18 or 19 base pairs (depending upon the clone) not predicted by the yeast Phe-tRNA sequence. These intervening segments are nearly identical in the three clones and are located within the structural gene, two base pairs from the nucleotides coding for the tRNA anticodon.
TL;DR: Investigations of the cellular and viral biosynthesis, in which compounds in this class of benzimidazoles possess the unique biological activity of selective inhibition of the synthesis of nuclear heterogeneous RNA, are reviewed.
Abstract: Publisher Summary This chapter brings together in a systematic way the recent work as well as some of the earlier studies on the mode of action of halogenated ribofuranosylbenzimidazoles on cellular and viral biosynthesis. Investigations of the cellular and viral biosynthesis, in which these compounds have been used as exploratory tools are also reviewed in this chapter. Compounds in this class of benzimidazoles possess the unique biological activity of selective inhibition of the synthesis of nuclear heterogeneous RNA (hnRNA) in cells of cold-blooded animals, including insects and in cells of avian and mammalian species. Because of the universality of the synthesis of hnRNA in animal species and because a portion of hnRNA sequences becomes mRNA, the action of halobenzimidazole ribosides on cellular biosynthesis is of broad interest. The action of these derivatives is also relevant to the process of transcription of the viral genomes of certain RNA and DNA viruses. In addition, this chapter briefly discusses three groups of structurally distinct bcnzimidazolcs that possess biological actions entirely different from those of halobenzimidazole ribosides: 2-(α-hydroxybenzyl) benzimidazole and certain related compounds are selective inhibitors of picornavirus multiplication; 5-methyl-2-D-ribobenzimidazole and congeners and 5-hydroxy-l-methylbenzimidazole and certain related compounds restore the capacity of chorioallantoic membranes from older chicken embryos to produce influenza virus in high yield.
TL;DR: In eucaryotic cells virtually all of the DNA is complex with proteins to form a unit fiber approximately 100 A in diameter, and Chromatin is formed by the higher order coiling of the unit fiber.
Abstract: In eucaryotic cells virtually all of the DNA is complex with proteins to form a unit fiber approximately 100 A in diameter. Chromatin is formed by the higher order coiling of the unit fiber. In procaryotic cells, as exemplified by E. coli, the actual structure of the chromosome is less clear (218), but the discovery of the DNA gyrase raises the possibility that the DNA helix in the cell is maintained in an underwound state. It may be important to consider these structural features of DNA in future biochemical studies on replication, transcription, and recombination. The recent discoveries of the DNA swivelases, the DNA gyrase, and the DNA unwinding enzymes considerably increase our knowledge of DNA biochemistry. As more is learned about these enzymes and their interaction with DNA, the prospects for understanding the details of DNA transcription, DNA recombination, and particularly DNA replication appear to be good.
TL;DR: The number of RNA species transcribed from the Ad2 chromosome between coordinates 29 and 50 exceeds the number of identified Ad2 proteins, and the diversity of splicing patterns and the variety of recombined sequences generated during the synthesis of late Ad2 mRNAs are emphasized.
TL;DR: The interactions of polymerase with ss DNA are, in general, stronger than the nonspecific interations of the enzyme with ds DNA, and the possibility of a modulating role of ion concentrations in the control of transcription is suggested.
Abstract: We have investigated the nonspecific interactions of Escherichia coli RNA polymerase core and holoenzyme with double-stranded (ds) and single-stranded (ss) DNA. Binding constants for these interactions as functions of such solution variables as monovalent and/or divalent cation concentration, temperature, or pH were determined by the method of deHaseth et a. [deHaseth, P.L., Gross, C.A., Burgess, R.R. and Record, M.T. (1977), Biochemistry 16, 4777--4783] from analysis of the elution of the proteins from small columns containing immobilized DNA. This technique, although as yet empirical, has been demonstrated to yield accurate binding constants fot the nonspecific interation of lac repressor with ds DNA. We find that observed binding constants (Kobsd) are extraordinarily sensitive functions of the monovalent cation concentration for the interactions of both core and holoenzyme with ds DNA. In the absence of divalent cations, the derivatives --(d log Kobsd/d log [Na+]) are 11 +/- 2 for the holo--ds DNA interaction and 21 +/- 3 for the core--ds DNA interaction. Consequently, approximately 11 and 21 low-molecular-weight ions are released, iin the thermodynamic sense, in the formation of the holo--ds and core--ds complexes, respectively (Record, M.T., Jr., Lohman, T.M., and deHaseth, P.L. (1976), J. Mol. Biol. 107, 145--158; Record, M.T., Jr., Anderson, C.F., and Lohman, T.M. (1978), Q. Rev. Biophys., in press). Ion release is a thermodynamic driving force for these nonspecific interactions and causes the stability of the complexes to increase very substantially with a reduction in monovalent ion concnetration. Possible molecular models which account for the different salt sensitivities of the holo--ds and core--ds complexes are discussed. Effects of the competitive ligand Mg2+ on these interactions are also examined. Substantial ion release (approximately 18 monovalent ions) also accompanies the interaction of either holo or core polymerase with ss DNA. Over the range of ion concentrations investigated the holo--ss interaction is substantially stronger than the core--ss interaction; furthermore, we conclude that the interactions of polymerase with ss DNA are, in general, stronger than the nonspecific interations of the enzyme with ds DNA. It is likely that the nonspecific interactions of RNA polymerase with DNA have physiological relevance. Not only is it plausible to assume that the same regions of the protein are involved in both specific and nonspecific interactions, but in addition nonspecific interactions of RNA polymerase and DNA may play role in determining the availability of this protein, in both the thermodynamic and the kinetic sense, for promoter binding and RNA chain initiation [von Hippel. P.H., Revzin, A., Gross, C.A., and Wang, A.C. (1974), Proc. Natl. Acad. Sci U.S.A. 71, 4808--4812]. Consequently, the strong dependences of the nonspecific interactions of RNA polymerase on ionic conditions suggest the possibility of a modulating role of ion concentrations in the control of transcription.
TL;DR: Theoretical and Experimental Background, Conversions of UV Inactivation Cross Sections into Transcriptional Distances, and Calibrations involving hybridization of RNA to DNA fragments from one and the same are reviewed.
Abstract: INTRODUCTION Historical Background . Theoretical and Experimental Background . UV Efficts on the Transcriptional Functions of DNA Templates . Dose-Effect Relationships. . Conversions of UV Inactivation Cross Sections into Transcriptional Distances ....... . The precursor to the ribosomal RNAs as an internal standard . Heterogeneous nuclear RNA . Calibrations using the reduction in overall RNA synthesis . Calibrations involving hybridization of RNA to DNA fragments from one and the same
TL;DR: The heat shock loci of Drosophila melanogaster chromosome subdivisions 87A and 87C have been studied by using cloned DNA and in situ hybridization to chromosomal RNA shows that transcripts of this sequence accumulate at both sites after temperature elevation.
Abstract: The heat shock loci of Drosophila melanogaster chromosome subdivisions 87A and 87C have been studied by using cloned DNA. Both sites contain a number of copies of a 2,4-kilobase (kb) region homologous to mRNA for the 70,000-dalton heat shock protein. In situ hybridization to chromosomal RNA shows that transcripts of this sequence accumulate at both sites after temperature elevation. At 87C there is a 1.5-kb repeated sequence homologous to another heat shock RNA. One cloned segment includes two to three tandem copies of this sequence located 0.8 kb from the beginning of a 2.4-kb message region. RNA complementary to the 1.5-kb repeat acccumulates at 87C after temperature elevation, but does not code for any known heat shock protein. In the sibling species D. simulans, there are sequences located and transcribed at 87A and 87C that are homologous to the melanogaster 2.4-kb message sequence. The 1.5-kb repeat, however, is absent from 87C in simulans and no heat shock RNA homologous to it can be detected.
TL;DR: Temperature-sensitive mutants of vesicular stomatitis virus (VSV) belonging to complementation group III contain a lesion in the matrix (M) protein that results in a 2--5 fold increase in transcription at the nonpermissive temperature.
TL;DR: The degree to which nuclear sequences are shared between tissues is estimated to be between 1–3 copies per cell of the diverse class of nuclear RNAs in brain, liver and kidney, suggesting that the great majority of nuclear RNA sequences homologous to single-copy DNA are held in common between these tissues and form a "nested" set of mutually inclusive sequences.
TL;DR: It is suggested that DRB acts not as an inhibitor of RNA chain initiation, but rather causes ‘premature’ chain termination close to the promoter, which may mean that RNA sequences near promoter sites that are responsible for mRNA formation can be isolated from DRB-treated cells.
Abstract: Exposure of HeLa cells to 5, 6-dichloro-1-β-D-ribofura-nosylbenzimidazde (DRB) late in the course of adenovirus 2 infection results in the inhibition of virus-specific RNA synthesis from all parts of the previously identified, very long (∼ 28 kilobases) late transcriptional unit, except for the first ∼ 400–800 nucleotides. It is suggested that DRB acts not as an inhibitor of RNA chain initiation, but rather causes ‘premature’ chain termination close to the promoter. A practical aspect of these findings may be that RNA sequences near promoter sites that are responsible for mRNA formation can be isolated from DRB-treated cells.
TL;DR: In this article, a 5′-specific probe was made by purifying a discrete 50 nucleotide-long reverse transcript attached to its tRNA primer, which was found to hybridize to RNA of the size of glycoprotein mRNA.
TL;DR: Results indicate that DNA gyrase is involved in transcription in phage promoter-dependent transcription of the trp operon in Φ80ptrp but not transcription from the authentic trp promoter.
Abstract: Nalidixic acid, novobiocin and coumermycin specifically inhibit phage promoter-dependent transcription of the trp operon in Φ80ptrp but not transcription from the authentic trp promoter. The nalidixic acid inhibition is not observed in an E. coli strain containing a nalAr mutation. These results indicate that DNA gyrase is involved in transcription.
TL;DR: In this report, in vitro synthesis of a facsimile of an in vivo transcript directed by deproteinized DNA in a mammalian cell-free postmitochondrial supernatant system is demonstrated.
Abstract: A cell-free system developed from human KB cells was used to transcribe 5.5S RNA from deproteinized adenovirus DNA in vitro. The cell-free RNA synthesis is dependent upon exogenous templates, ribonucleoside triphosphates, and cell-free postmitochondrial supernatant of human KB cells. The synthesis of 5.5S RNA is inhibited only by high levels of alpha-amanitin; therefore it is carried out by RNA polymerase III. The rate of synthesis was linear for at least 2 hr, indicating reinitiation. The 5.5S RNA synthesized in vitro is similar to the corresponding in vivo RNA in size, sequence, and coding region on adenovirus type 2 DNA. In this report is demonstrated in vitro synthesis of a facsimile of an in vivo transcript directed by deproteinized DNA in a mammalian cell-free postmitochondrial supernatant system.
TL;DR: With phage G4 DNA as template, primase (the dnaG protein) synthesizes a 26- to 29-residue RNA transcript at the origin of replication that contains a hairpin region of one A-U and seven G-C base pairs.
TL;DR: A plasmid is constructed that permits a unique 5'-end labeling of each strand of a 95-base-pair fragment containing a lac operon promoter and shows that the polymerase unwinds the helix at the origin of transcription.
Abstract: The chemical alkylating agent dimethyl sulfate can probe the interaction between Escherichia coli RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase, EC 2.7.7.6) and the purine bases of a promoter. This agent methylates the N7 position on guanine or the N3 position on adenine; the bound protein can either protect these positions or affect the reactivity to produce an enhanced methylation. The pattern of DNA residues in the lactose promoter protected from, or enhanced to, methylation by a specifically bound polymerase shows that the enzyme covers a region of at least 38 base pairs, stretching upstream from the origin of transcription. These protein-DNA contacts occur predominantly in the major groove of the DNA helix. Furthermore, this pattern of methylation shows that the polymerase unwinds the helix at the origin of transcription. The relationship between polymerase-DNA contacts defined by dimethyl sulfate and known features of promoter structure is discussed. To facilitate these experiments I have constructed a plasmid that permits a unique 5'-end labeling of each strand of a 95-base-pair fragment containing a lac operon promoter. This plasmid contains two copies of the lac promoter-operator region.
TL;DR: The results show that this gene may be transcribed with remarkable fidelity in injected oocytes, and that untranscribed genes are converted into a characteristic chromatin structure.
Abstract: DNA CLONING and the direct visualisation of chromatin transcription by electron microscopy provide useful details of the structure and function of genes, but the value of these techniques would be even greater if they could be applied to the same genes or segments of DNA. Our previous work1 on amplified ribosomal DNA (rDNA) of the water beetle Dytiscus showed that rDNA injected into oocytes is correctly transcribed. Gradients of growing rRNA fibrils could be unambiguously recognised as correct transcription when compared to the characteristic transcription pattern observed in the original cell type. We have now extended the usefulness of this technique to recombinant DNA, choosing as an example of a cloned vertebrate gene a single rDNA repeat of Xenopus laevis contained in plasmid DNA. The results show that this gene may be transcribed with remarkable fidelity in injected oocytes, and that untranscribed genes are converted into a characteristic chromatin structure.